6XPW

Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to CDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.133 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Nucleoside selectivity of Aspergillus fumigatus nucleoside-diphosphate kinase.

Nguyen, S.Jovcevski, B.Pukala, T.L.Bruning, J.B.

(2021) FEBS J 288: 2398-2417

  • DOI: https://doi.org/10.1111/febs.15607
  • Primary Citation of Related Structures:  
    6XP4, 6XP7, 6XPS, 6XPT, 6XPU, 6XPV, 6XPW

  • PubMed Abstract: 

    Aspergillus fumigatus infections are rising at a disconcerting rate in tandem with antifungal resistance rates. Efforts to develop novel antifungals have been hindered by the limited knowledge of fundamental biological and structural mechanisms of A. fumigatus propagation. Biosynthesis of NTPs, the building blocks of DNA and RNA, is catalysed by NDK. An essential enzyme in A. fumigatus, NDK poses as an attractive target for novel antifungals. NDK exhibits broad substrate specificity across species, using both purines and pyrimidines, but the selectivity of such nucleosides in A. fumigatus NDK is unknown, impeding structure-guided inhibitor design. Structures of NDK in unbound- and NDP-bound states were solved, and NDK activity was assessed in the presence of various NTP substrates. We present the first instance of a unique substrate binding mode adopted by CDP and TDP specific to A. fumigatus NDK that illuminates the structural determinants of selectivity. Analysis of the oligomeric state reveals that A. fumigatus NDK adopts a hexameric assembly in both unbound- and NDP-bound states, contrary to previous reports suggesting it is tetrameric. Kinetic analysis revealed that ATP exhibited the greatest turnover rate (321 ± 33.0 s -1 ), specificity constant (626 ± 110.0 mm -1 ·s -1 ) and binding free energy change (-37.0 ± 3.5 kcal·mol -1 ). Comparatively, cytidine nucleosides displayed the slowest turnover rate (53.1 ± 3.7 s -1 ) and lowest specificity constant (40.2 ± 4.4 mm -1 ·s -1 ). We conclude that NDK exhibits nucleoside selectivity whereby adenine nucleosides are used preferentially compared to cytidine nucleosides, and these insights can be exploited to guide drug design. ENZYMES: Nucleoside-diphosphate kinase (EC 2.7.4.6). DATABASE: Structural data are available in the PDB database under the accession numbers: Unbound-NDK (6XP4), ADP-NDK (6XP7), GDP-NDK (6XPS), IDP-NDK (6XPU), UDP-NDK (6XPT), CDP-NDK (6XPW), TDP-NDK (6XPV).


  • Organizational Affiliation

    Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase162Aspergillus fumigatus Af293Mutation(s): 0 
Gene Names: ndk1AFUA_5G03490
EC: 2.7.4.6
UniProt
Find proteins for Q7Z8P9 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore Q7Z8P9 
Go to UniProtKB:  Q7Z8P9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z8P9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.133 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.694α = 90
b = 101.8β = 90
c = 113.898γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description